You are right, :4.SG<:5.0&.C works: I used 'CO' instead of 'C'. Now I get:
ACTION SETUP FOR PARM '../mut1_2w_noWATCl.prmtop' (1 actions):
0: [distance 4SG :4.SG :4.SG<:5.0&@C out 4SG.dist noimage]
:4.SG (1 atoms) to :4.SG<:5.0&@C (7 atoms), imaging off.
Thank you.
Krisztina
Quoting Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> On Sat, Jul 5, 2014 at 8:18 AM, Krisztina Fehér <Krisztina.Feher.ugent.be>
> wrote:
>
>>
>> :4.SG<:5.0&.C
>>
>
> This mask seems valid. Did you receive an error message when you used it?
>
> -Dan
>
>
>>
>> which did not work and would like to know why. Is there a limitation
>> in the use of the logical operators?
>>
>> Thank you,
>> Krisztina
>>
>>
>>
>>
>>
>>
>>
>>
>> Quoting Daniel Roe <daniel.r.roe.gmail.com>:
>>
>> > Hi,
>> >
>> > On Fri, Jul 4, 2014 at 3:48 AM, Krisztina Fehér <
>> Krisztina.Feher.ugent.be>
>> > wrote:
>> >
>> >> circle. I wonder if I could rather use the distance action command. I
>> >> tried this:
>> >>
>> >> distance 4CB :4.CB :*.C out 4CBtoCO.dist noimage
>> >>
>> >> but it averages all distances into one distance:
>> >>
>> >
>> > It's actually the distance between the the first atom and the center of
>> > mass of the atoms selected by ':*.C' (note that the :* is not necessary
>> as
>> > .C implies :*).
>> >
>> > You can generate the input you need relatively easily via a script.
>> Cpptraj
>> > has several command-line flags which allow you to access the mask parser
>> in
>> > various ways. For example you could use something like (in bash):
>> >
>> > for ATOM in `cpptraj -p topology.parm7 -ms '.C'` ; do
>> > if [[ $ATOM != "Selected=" ]] ; then
>> > echo "distance 4CB_$ATOM :4.CB @$ATOM out 4CBtoCO.dist noimage" >>
>> > cpptraj.in
>> > fi
>> > done
>> >
>> > Hope this helps,
>> >
>> > -Dan
>> >
>> >
>> >
>> >> Frame 4CB
>> >> 1 8.6029
>> >> 2 8.9513
>> >> 3 8.9097
>> >> 4 8.6357
>> >> 5 8.4419
>> >> 6 8.7178
>> >> ....
>> >>
>> >> Is there some way to force cpptraj to iterate over the atoms in the
>> mask?
>> >>
>> >>
>> >> Thanks,
>> >> Krisztina
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> > Dear All,
>> >> >
>> >> > I would like to qualitatively understand which other atoms could
>> >> > potentially affect the 13C chemical shift of :4.CG via anisotropic
>> >> > shielding effects. For this reason I am looking for an analysis
>> >> > command, which would enable me to list all atoms within a certain
>> >> > threshold around a particular atom (let's say :4.CG) during the
>> >> > trajectory. I am searching for something similar to
>> >> > Action/modfiy/around/atoms withing 5A function in Pymol, just
>> >> > applied to a whole trajectory. I was trying the contact command in
>> >> > ccptraj, but it generated either contacts from all atoms to all atoms:
>> >> >
>> >> > contacts first out contact.out distance 5
>> >> >
>> >> >
>> >> > or certain atoms to certain atoms:
>> >> >
>> >> > contacts first out contacts.out distance 5 @CG
>> >> >
>> >> > while I would like to have :4.CG to all atoms (or maybe only to
>> >> > carbonyl or nitrogen groups).
>> >>
>> >> Perhaps a mask that selects based on a distance criteria will work?
>> >>
>> >> Something like "(:4.CG<.5.0)" will select all atoms within 5 angstroms
>> >> of the CG atom of residue 4. Replacing @5.0 with :5.0 will select all
>> >> residues within 5 Angstroms of the CG atom of residue 4.
>> >>
>> >> You can use the "mask" command in cpptraj to write a list of atoms
>> >> that satisfy the criteria. In general, masks are evaluated once at
>> >> the beginning (on the reference structure or first frame), but I think
>> >> the "mask" command is different in this regard and evaluates the mask
>> >> for every frame. Dan can correct me if I'm wrong here.
>> >>
>> >> Hope this helps,
>> >> Jason
>> >>
>> >> --
>> >> Jason M. Swails
>> >> BioMaPS,
>> >> Rutgers University
>> >> Postdoctoral Researcher
>> >>
>> >> ----- End forwarded message -----
>> >>
>> >>
>> >>
>> >> _______________________________________________
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>> >>
>> >
>> >
>> >
>> > --
>> > -------------------------
>> > Daniel R. Roe, PhD
>> > Department of Medicinal Chemistry
>> > University of Utah
>> > 30 South 2000 East, Room 201
>> > Salt Lake City, UT 84112-5820
>> > http://home.chpc.utah.edu/~cheatham/
>> > (801) 587-9652
>> > (801) 585-6208 (Fax)
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Jul 05 2014 - 08:30:02 PDT
